A methodology of generating time-domain reduced-order models of viscous lateral damping effects for microsystems is presented. A three-dimensional finite-difference-method (FDM) Stokes flow solver was developed and verified. The system matrices generate by the solver were then reduced to low-order macromodels, which can be easily inserted into a system-level modeling package for transient and frequency analysis. The simulated results of the FDM Stokes solver and the reduced-order macromodels are verified with the analytical solution. The reduced-order models have been seen to be about two-order-of-magnitude as efficient as the FDM solver. Transient simulations also indicate that friction stress of 3D model results in more damping effects than those estimated by the 1-D analytical models.